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MB Sample ID: SA092113
| Local Sample ID: | GLD020 |
| Subject ID: | SU001336 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Gender: | Male and female |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU001336 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Gender: | Male and female |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| GLD020 | SA092113 | FL013206 | Positive | HIV |
Collection:
| Collection ID: | CO001330 |
| Collection Summary: | During a clinic visit, blood was drawn from HIV positive individuals and controls as previously described as part of a larger study of differences in the fecal microbiome in HIV positive and high risk populations [Caporaso JG, et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods. 2010;7:335–6. doi:10.1038/nmeth.f.303]. |
| Sample Type: | Blood (plasma) |
| Storage Conditions: | -80℃ |
Treatment:
| Treatment ID: | TR001351 |
| Treatment Summary: | Three cohorts based on HIV status: (1) HIV-1 infection untreated; (2) chronic HIV-1 infection on long-term ART; (3) healthy controls (HIV-negative individuals both high and low risk for contracting HIV). |
Sample Preparation:
| Sampleprep ID: | SP001344 |
| Sampleprep Summary: | 100 µL of plasma spiked with internal standards underwent a protein crash with 400 µL ice cold methanol. The supernatant was dried under nitrogen. Methyl tert-butyl ether (MTBE) and water were added to extract the hydrophobic and hydrophilic compounds, respectively. The upper hydrophobic layer was transferred to a new tube and the lower hydrophilic layer was re-extracted with MTBE. The upper hydrophobic layer was combined, dried under nitrogen and reconstituted in 200 µL of methanol. The hydrophilic layer was dried under nitrogen, underwent a second protein crash with water and ice-cold methanol (1:4 water-methanol). The supernatant was removed, dried by SpeedVac at 45 °C and reconstituted in 100 µL of 5% acetonitrile in water. Both fractions were stored at -80 °C until LCMS analysis. |
| Processing Storage Conditions: | On ice |
Combined analysis:
| Analysis ID | AN002105 | AN002106 | AN002107 | AN002108 |
|---|---|---|---|---|
| Analysis type | MS | MS | MS | MS |
| Chromatography type | Reversed phase | Reversed phase | HILIC | HILIC |
| Chromatography system | Agilent 1290 | Agilent 1290 | Agilent 1290 | Agilent 1290 |
| Column | Agilent Zorbax RRHD SB-C18 (100 x 2.1mm,1.8um) | Agilent Zorbax RRHD SB-C18 (100 x 2.1mm,1.8um) | Phenomenex Kinetex HILIC 100A (50 x 2.1 mm,2.6um) | Phenomenex Kinetex HILIC 100A (50 x 2.1 mm,2.6um) |
| MS Type | ESI | ESI | ESI | ESI |
| MS instrument type | QTOF | QTOF | QTOF | QTOF |
| MS instrument name | Agilent 6520 QTOF | Agilent 6520 QTOF | Agilent 6550 QTOF | Agilent 6550 QTOF |
| Ion Mode | POSITIVE | NEGATIVE | POSITIVE | NEGATIVE |
| Units | Abundance | Abundance | Abundance | Abundance |
Chromatography:
| Chromatography ID: | CH001537 |
| Chromatography Summary: | Gradient was as follows: 0–1 minutes 30–70% B, 1–7.92 minutes 70–100% B, 7.92–10.4 minutes 100% B, 10.4–10.5 minutes 100–30% B, 10.5–15.1 minutes 30% B. |
| Instrument Name: | Agilent 1290 |
| Column Name: | Agilent Zorbax RRHD SB-C18 (100 x 2.1mm,1.8um) |
| Column Temperature: | 60 °C |
| Flow Rate: | 0.7 mL/min |
| Injection Temperature: | 4 °C |
| Solvent A: | 100% water; 0.1% formic acid |
| Solvent B: | 60% isopropanol/36% acetonitrile/4% water; 0.1% formic acid |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH001538 |
| Chromatography Summary: | Gradient elution was as follows: 0–2 minutes 100% B, 2–2.1 minutes 100–90% B, 2.1–8.6 minutes 90–50% B, 8.6–8.7 minutes 50–0% B, 8.7–14.7 minutes 0% B, 14.7–14.8 minutes 0–100% B, 14.8–24.8 minutes 100% B. |
| Instrument Name: | Agilent 1290 |
| Column Name: | Phenomenex Kinetex HILIC 100A (50 x 2.1 mm,2.6um) |
| Column Temperature: | 20 °C |
| Flow Rate: | 0.6 mL/min |
| Injection Temperature: | 4 °C |
| Solvent A: | 50% acetonitrile/50% water; ammonium acetate, pH 5.8 |
| Solvent B: | 90% acetonitrile/10% water; pH 5.8 ammonium acetate |
| Chromatography Type: | HILIC |
MS:
| MS ID: | MS001956 |
| Analysis ID: | AN002105 |
| Instrument Name: | Agilent 6520 QTOF |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| MS Comments: | Scan range 50-1700 m/z, scan rate 2.2 spectra/sec, gas temp 300C, gas flow 12 L/min, nebulizer 30 psig, Vcap 4000 V, fragmentor 120 V. Data processed with Profinder B.08 using small molecule chromatographic extraction. |
| Ion Mode: | POSITIVE |
| MS ID: | MS001957 |
| Analysis ID: | AN002106 |
| Instrument Name: | Agilent 6520 QTOF |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| MS Comments: | Scan range 50-1700 m/z, scan rate 1.0 spectra/sec, gas temp 300C, gas flow 12 L/min, nebulizer 30 psig, Vcap 4000 V, fragmentor 120 V. Data processed with Profinder B.08 using small molecule chromatographic extraction. |
| Ion Mode: | NEGATIVE |
| MS ID: | MS001958 |
| Analysis ID: | AN002107 |
| Instrument Name: | Agilent 6550 QTOF |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| MS Comments: | Scan range 75-1700 m/z, scan rate 2.0 spectra/sec, gas temp 225C, gas flow 18 L/min, nebulizer 45 psig, Vcap 3500 V, fragmentor 360 V. Data processed with Profinder B.08 using small molecule chromatographic extraction. |
| Ion Mode: | POSITIVE |
| MS ID: | MS001959 |
| Analysis ID: | AN002108 |
| Instrument Name: | Agilent 6550 QTOF |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| MS Comments: | Scan range 75-1700 m/z, scan rate 2.0 spectra/sec, gas temp 225C, gas flow 18 L/min, nebulizer 45 psig, Vcap 3500 V, fragmentor 360 V. Data processed with Profinder B.08 using small molecule chromatographic extraction. |
| Ion Mode: | NEGATIVE |
